DNMT3B drives neuroendocrine lineage plasticity and aggressive progression in prostate cancer

Neuroendocrine prostate cancer (NEPC) is an aggressive and therapy-resistant subtype of advanced prostate cancer characterized by poor prognosis and limited treatment options. Enzalutamide, an androgen receptor (AR) pathway inhibitor, is a standard second-line therapy for prostate adenocarcinoma (PrAd). However, enzalutamide resistance (EnzR) promotes not only neuroendocrine differentiation (NED) but also the induction of stemness-associated programs in PrAd cells. We identified the de novo DNA methyltransferase DNMT3B as a stemness-related gene upregulated in EnzR-PrAd cells and found that its expression is further significantly elevated in NEPC compared with PrAd. Our studies reveal that DNMT3B is a critical driver of NEPC development by coordinating the regulation of neuroendocrine and stemness transcriptional networks. Genetic inhibition of DNMT3B suppresses NEPC cell proliferation by impairing cell-cycle progression and triggering apoptosis both in vitro and in vivo. DNMT3B loss altered NED-associated, stemness, and epithelial-associated genes. We further uncover a reciprocal regulatory relationship between DNMT3B and the neuroendocrine transcriptional repressor REST. Using a human prostate cell transformation model that recapitulates NEPC evolution, we demonstrate that DNMT3B is required for both the initiation and maintenance of the NEPC phenotype. Finally, pharmacologic inhibition of DNMT3B with the selective inhibitor Nanaomycin A reduces NEPC tumor growth and suppresses NED and stemness marker expression without apparent acute toxicity in vivo. Implications: DNMT3B drives therapy-induced lineage plasticity in prostate cancer, and its inhibition suppresses NEPC growth and differentiation, highlighting it as a promising therapeutic target for treatment-resistant disease.